The Panda's Thumbtag:pandasthumb.org,2008-04-25://22015-07-30T20:16:51ZThe Panda's Thumb is the virtual pub of the University of Ediacara. The patrons gather to discuss evolutionary theory, critique the claims of the antievolution movement, defend the integrity of both science and science education, and share good conversation.Movable Type Pro 4.381Domesticated: Book reviewtag:pandasthumb.org,2015://2.71172015-07-25T14:00:00Z2015-07-30T20:16:51ZA number of years ago, I found a family of raccoons living in my chimney.1 I got them out by dropping a trouble light down the flue and turning it on for a few days. According to Richard C. Francis, in his splendid book, Domesticated, animals such as raccoons living in urbanized areas represent the first step toward domesticating those animals. The full title of the book is Domesticated: Evolution in a Man-Made World, and...Matt Younghttp://www.mines.edu/~mmyoung

A number of years ago, I found a family of raccoons living in my chimney.1 I got them out by dropping a trouble light down the flue and turning it on for a few days. According to Richard C. Francis, in his splendid book, Domesticated, animals such as raccoons living in urbanized areas represent the first step toward domesticating those animals.

The full title of the book is Domesticated: Evolution in a Man-Made World, and Francis shows in considerable detail how various animals became domesticated: dogs, cats, pigs, sheep and goats, reindeer, camels, horses, rodents, and perhaps humans, as well as other predators such as raccoons and ferrets. Each scenario is slightly different, each seems well documented, and each has just a little bit of just-so story in it.

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The audience for the book is not completely clear. I think the author thinks that the book is written for the lay reader, but at times it got a little hairy, and I recommend that, if you are not a biologist, you keep your computer nearby. Or, if you are younger than I, your smart phone. Indeed, after getting through 50 or so pages of the complimentary copy I received, I bought a Kindle edition, precisely so that I could more easily look up terms that were unfamiliar or not entirely familiar. Lest this paragraph be taken as a criticism, let me make clear that the effort was wholly worthwhile.

Francis begins with the now well known domestication of foxes by Dmitry Belyaev in Siberia. Belyaev and his colleagues selected foxes, as Francis puts it, “for one trait and one trait only: the capacity to tolerate human proximity without fear or aggression.” In approximately 50 years, they bred foxes that were as tame as many dogs. But there were concomitant physical changes: hair became mottled or piebald, ears flopped, tails curled, snout and limbs shortened, and face broadened, for example. Additionally, brain volume and sexual dimorphism were reduced. Many of the same physical changes may be seen in domesticated dogs, cats, horses, cattle – and all are a direct result of selection for tameness. Such by-products are a general feature of evolution and are a form of convergent evolution resulting from various homologies that more or less guarantee that all domesticated mammals will evolve similar traits.

The raccoons in my chimney are probably already self-selected for tolerance of human beings. Wolves probably self-selected in roughly the same way: perhaps they began to domesticate themselves by feeding on scraps left by early humans, as the raccoons occasionally feed on my garbage. Wolves in different geographical areas evolved into landraces, sort of proto-breeds that eventually developed into what we know as breeds.

I was surprised to learn that the concept of breed is only a century or so old. British kennel clubs, beginning in the 1870’s, hyper-selected for various traits, such as the snout of a bulldog. Francis says that they routinely mated a champion male with his own female offspring and remarks somewhat archly that the Victorian aristocrats ultimately responsible for such incestuous relationships may have been desensitized as a result of their own pedigrees.
Besides causing inbreeding, such selection also caused serious physical and genetic defects in virtually all purebred dogs. Not to mention that thoroughbred horses, which Francis deals with in a later chapter, are at an evolutionary dead end: they are infertile, and their speed has not improved in 50 years. There are no master races; they need to be mongrelized.

Cats also enjoyed a commensal relationship with humans, probably after the mouse was introduced into the wild cats’ region. Although humans consider cats somewhat standoffish, Francis notes that feral housecats remain far more tame and far more gregarious than their wild ancestors. Like dogs, cats have been bred to have various skeletal deformities, a practice that Francis considers “unconscionable.”

Pigs may have been domesticated similarly to dogs, but it is also possible that pigs, cattle, sheep, goats, and horses were domesticated by “human management of wild populations,” wherein wild animals were first herded, then bred. Cows, in particular, descend from the wild aurochs, a large, fierce beast that Caesar compared, with some hyperbole, to elephants. Regarding the aurochs’s ferocity, Francis writes,

[N]o matter how tame these early domesticates were, by auroch[s] standards, you would still need to be a lot braver than a bull leaper to push their calves aside and pull on their teats.

(What’s not to like about a book that regularly comes up with quips like these?) Francis seems to have forgotten, however, that elephants have been domesticated, and he writes that the aurochs is the largest domesticated animal. Oddly, he thinks (incorrectly) that the singular of aurochs is auroch. In fact, the singular is aurochs; the word is cognate with ox (think ur-ox). It is odd that the copy editor did not catch this mistake, because the book seems to be generally well prepared (we will not, however, discuss the use of grizzly where grisly was meant).

Sheep and goats (Francis prefers goats), reindeer, camels, horses, rodents: Francis covers them all, often beginning a chapter with a curious anecdote. Horses, for example, were originally domesticated for their meat; only later, after other meat sources were available, was the horse used for transportation and warfare. The horse’s status has risen so sharply that most Europeans and their cultural descendants “would be about as aghast at the thought of eating horse meat as they would dog meat.”

Francis devotes 2 chapters to the question whether humans domesticated themselves. The argument is long, and I am afraid you will have to read it for yourself, but it depends in part on the argument that humans, like other domesticated animals, are neotenous, that is, the adult animal retains juvenile features, such as big eyes. I got slightly bogged down in one chapter by the profusion of terms like hominid, hominin, hominine, and hominoid (which I think of as homonym-oids). The second of these chapters asks whether human hypersociality came as the result of self-domestication by way of natural selection for tameness. Answer: “It ain’t necessarily so”; Francis wants more evidence.

The final chapter, except for an epilogue, is called “The Anthropocene” and asks how an utterly obscure, bipedal, nearly hairless ape could in a mere few hundred thousand years come to dominate the planet and indeed be responsible for the most recent mass extinction. I cannot go into detail here, but I am left with the feeling that it was mostly “cultural evolution,” with biological evolution following thereafter – as when herdsmen begin to use dairy products (cultural evolution) and only thereafter does an allele for lactose tolerance predominate (biological evolution).
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Appendix 1. I resolved not to read the appendixes; generally I do not like appendixes or endnotes1 and think that a topic should be incorporated into the book if it is important enough and dropped if it is not (excluding very abstruse derivations and whatnot). Nevertheless, I began to read the appendixes and was treated to a discussion of the need for a new synthesis that gets away from the gene-centered view popularized by Richard Dawkins, a serious and hard-hitting critique of evolutionary psychology, and also some boring stuff.

Appendix 2. As one of the self-appointed guardians of the modern metric system, I disliked the book’s use of “mya” for “million years ago”; if anything, the usage should have been “Mya.” But that is not really satisfactory either, because “y” and “a,” though not SI symbols, are both commonly used as a symbol for “year.” I probably would have used “Ma” for “megannus,” since “year” is Anglocentric.

In addition, when he means tens or hundreds of thousands of years, the author uses “BP,” presumably meaning “before present,” which is arguably OK, but not consistent with the previous usage. At least once, he used “CE,” which is perhaps more useful than “BP” when we are discussing more or less historical times, but again is inconsistent.
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1 My son also had a raccoon in his chimney; unfortunately, his died there, with unfortunate consequences involving maggots. I really did not want to tell you that, but I wanted to make a point about the endnotes. The book has a significant number of endnotes. Many of them simply cite a reference, but others have content. I find it very distracting to have to stop my reading and go to an endnote. Part of the art of writing is culling: if something was worth telling, the author should have worked it into the text or, otherwise, killed it.

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Luskin makes more mistakes on the Cambrian and Cladisticstag:pandasthumb.org,2015://2.71162015-07-23T01:23:28Z2015-07-23T04:54:57Z(edited to add a point on Aegirocassis and Parapeytoia) This week, the Discovery Institute Press put out another book called Debating Darwin’s Doubt. I took one for the team and bought it, in part because a a decent chunk of the book is responding to me. I’m pretty sure I’ve never been mentioned so much in a book! Sadly, though, looking through it, almost all of it is material re-hashed from the DI “Evolution News...Nick Matzkehttp://www.talkdesign.org

(edited to add a point on Aegirocassis and Parapeytoia)

This week, the Discovery Institute Press put out another book called Debating Darwin’s Doubt. I took one for the team and bought it, in part because a a decent chunk of the book is responding to me. I’m pretty sure I’ve never been mentioned so much in a book!

Sadly, though, looking through it, almost all of it is material re-hashed from the DI “Evolution News and Views” blog and is no better than it was the first time. There is, however, a new chapter (I think it is new) by Casey Luskin, chapter 9, “Cladistics to the Rescue?” responding to me. If you don’t want to buy the book, there is a free podcast at ID the Future (heh), “Debating Darwin’s Doubt: Casey Luskin on Classification of Organisms” that interviews Luskin (although I think he wrote the questions). It has mostly the same material.

Unfortunately, I do not have time at the moment to write the introductory-level-tutorial-from-square-one that would be required to really explain the basics of cladistics and phylogenetics to Luskin et al. I have literally just moved to Australia to start as a Discovery Early Career Researcher Award (DECRA) Fellow in the Division of Ecology, Evolution, and Genetics, Research School of Biology, at The Australian National University in Canberra. Once I have a bed and a computer in my office I may be in better shape to do things more thoroughly – I have a bit of a fantasy about writing an R vignette or R package called something like BasicPhylogeneticsForCreationistsEspeciallyLuskin (I’ll take suggestions on a better name/acronym).

However, below, I can briefly hit the high points on the small bit of Luskin’s chapter that was new.

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Except for chapter 9, everything else I’ve seen pertaining to me in Debating Darwin’s Doubt has already been addressed in previous posts:

Here is my main comment responding to Luskin’s chapter, “Cladistics to the Rescue?” This is modified from a comment on Larry Moran’s Sandwalk post.

Key flaws in Luskin’s chapter 9, “Cladistics to the rescue?”

(1) Lobopods aren’t a natural group. Luskin continues to think of “lobopods” as a coherent group, which results in pointless arguments about e.g. whether lobopods are “closer” to arthropods than anomalocarids. Earth to Luskin: lobopods are a paraphyletic grab-bag. Living arthropods, onychophorans, and tardigrades all descend from lobopods, as do anomalocarids. Phylogenetically speaking, then, all of these groups are *within* the lobopod group.

When Luskin quotes certain authorities (mostly the Erwin et al. Science paper) calling lobopods a “phylum” (if memory serves, Erwin et al. actually create two phyla out of lobopods, phyla which no one else recognizes IIRC, further illustrating the fundamental conceptual problems with applying ranked Linnaean taxonomy to fossils), he is ignoring what I explained previously about old-fashioned Linnaean taxonomy and the confusions it causes. Some (typically older) authors accept paraphyletic phyla. But it has long been clear that purely phylogenetic classification is taking over. It’s already dominant in most areas of biology/paleontology, and it’s just taken a bit longer with fossil invertebrates, although that is now clearly the leading edge in the field, even in the Cambrian Explosion research (see the work of Graham Budd, David Legg, etc.) You can’t quote authors talking about “phyla” from different taxonomic schools of thought, writing in different decades, etc. without understanding the differences in what they are referring to.

Sometimes it appears that Luskin actually means “onychophorans” or “crown + stem onychophorans” when he says “lobopods”. Some of what Luskin says would seem less crazy on that hypothesis. More on taxonomy below.

(2) Panarthropods and the importance of stem/crown terminology. In a similar vein, the new Luskin chapter contains a fair bit of discussion about how different the anomalocarids are from true arthropods, contradicting Meyer/Luskin’s previous arguments (repeated in this same book, in other chapters!) about how it was totally OK to lump anomalocarids in as just another thing in the arthropod group! (Another argument for phyla-schmyla! I thought phyla were supposed to be super-duper-distinct!)

Throughout the DI commentary (mostly Meyer/Luskin) discussing arthropods, we see confusion over “arthropods”, often evidenced in how Luskin deploys quotes. Sometimes by “arthropods” Luskin means panarthropods, sometimes he means crown-group arthropods, sometimes he means critters sharing “enough” arthropod traits. It is true that all of these usages can be found in the literature over the decades, and it’s true that it can be confusing, but THIS IS PRECISELY WHY RIGOROUS PHYLOGENETIC CLASSIFICATION, AND THE STEM/CROWN DISTINCTION, WAS INVENTED IN THE FIRST PLACE. It’s meaningless to quote-mine a bunch of quotes with people using slightly different terminology about, say, the position of Anomalocaris, and to pretend they all mean hugely different things. Typically they are just different ways of saying “on the arthropod stem”.

I’ve taken one position from the beginning, which is that anomalocarids are below the arthropod crown group (exactly how far below can be debated, but these are details), and this means they have transitional morphology. Everything else on the stem (dozens of fossil taxa, at the very least) also has transitional morphology. The transitional morphology is what places them on the stems, instead of inside crown arthropods or crown onychophorans. Thus there are many fossils with transitional morphology between crown-group phyla, and many of these fossils are in the early Cambrian. No, they don’t all have to appear in exact chronological order, like a children’s-cartoon version of evolution, because fossil sampling is a stochastic process, like taking a phylogenetic tree and sampling it by throwing darts at it, or (for lagerstatten) taking a number of samples at one time-point. There will be an overall correlation between phylogeny and fossil dates, which has been demonstrated in publications in many cases, but it won’t be exact. The fact that stem groups are so prevalent compared to crown groups in the early Cambrian is evidence of this time-phylogeny correlation in the Cambrian taxa specifically. But I’ve said all of this before, not sure why I am saying it again. In Darwin’s Doubt, Meyer missed this crucial transitional fossil data in epic fashion, and all of the subsequent discussion of this point by Meyer, Luskin et al. has been an attempt to avoid the key point: many transitional fossils are known from the early Cambrian.

(3) Anomalocarids and legs. Luskin makes much use of an argument along the lines of “lobopods have arthropod-like legs but no complex head; anomalocarids have an arthropod-like head but no legs (they have swimming flaps); this means the data conflict with the tree and therefore the whole thing is bunk and special creation is a better alternative” (I am paraphrasing, obviously. But that’s his argument.) Actually, if that were the data, only one extra change would necessarily need to be postulated, namely loss of legs in the anomalocarids, and adding one character change step to a cladistic reconstruction does no great violence to the data. IDists/creationists, being almost always hopeless amateurs who can’t be bothered to get to the library and really learn a topic, basically always think about the evolution of just a few characters, and judge scenarios on that basis. But in real life, cladistic analyses are typically done on hundreds of characters, and cladistic reconstructions will have hundreds or thousands of character steps in the most parsimonious tree. Having a step for leg loss is perfectly justified, if other characters support the tree topology in that region.

As if that weren’t enough, we have lots of evidence from all kinds of sources that events like limb loss happen occasionally, undoubtedly much more commonly than limb gain.

But – this whole discussion is pointless, because the anomalocarid or near-anomalocarid Parapeytoiahad friggin’ legs! And it’s early Cambrian (530 Ma)! Hello transitional form!

And, on top of that, earlier this year, to international acclaim, Aegirocassis was published. This guy is Ordovician (480 Ma), and is an anomalocarid, but the specimen is huge (2 meters), and some combination of the preservation and the size allowed the authors to notice that the flaps can actually be separated into dorsal and ventral flaps, and resolve other features of flap anatomy.

Exceptionally preserved fossils from the Palaeozoic era provide crucial insights into arthropod evolution, with recent discoveries bringing phylogeny and character homology into sharp focus. Integral to such studies are anomalocaridids, a clade of stem arthropods whose remarkable morphology illuminates early arthropod relationships and Cambrian ecology. Although recent work has focused on the anomalocaridid head, the nature of their trunk has been debated widely. Here we describe new anomalocaridid specimens from the Early Ordovician Fezouata Biota of Morocco, which not only show well-preserved head appendages providing key ecological data, but also elucidate the nature of anomalocaridid trunk flaps, resolving their homology with arthropod trunk limbs. The new material shows that each trunk segment bears a separate dorsal and ventral pair of flaps, with a series of setal blades attached at the base of the dorsal flaps. Comparisons with other stem lineage arthropods indicate that anomalocaridid ventral flaps are homologous with lobopodous walking limbs and the endopod of the euarthropod biramous limb, whereas the dorsal flaps and associated setal blades are homologous with the flaps of gilled lobopodians (for example, Kerygmachela kierkegaardi, Pambdelurion whittingtoni) and exites of the ‘Cambrian biramous limb’. This evidence shows that anomalocaridids represent a stage before the fusion of exite and endopod into the ‘Cambrian biramous limb’, confirming their basal placement in the euarthropod stem, rather than in the arthropod crown or with cycloneuralian worms.

For more commentary, see Edgecomb in Current Biology last month: “In a Flap About Flaps.” He appears to basically agree with the Nature authors, although he adds some more considerations about another specimen that may further illustrate the transition.

(4) The Consistency Index (CI) and null distributions Luskin has finally discovered the concept of a null distribution for the Consistency Index (CI)! It’s only taken him about 2 years! Now, finally, having learned about it, he can dimly see the problem with his/Meyer’s old tactic of squinting at some published CI value and declaring it “high” or “low” without any consideration of what the null distribution is. So, his new argument is that the null hypothesis of random distribution of characters is silly. To that I say – why? That is precisely what one is claiming if one claims the data have no cladistic tree structure, which is precisely what these turkeys have been telling their readers for years now. (Except Berlinski; he admitted at one point that there is tree structure in the data, which is not made up.)

Luskin then raises the idea that intelligent design could correlate some characters, and this could cause above-null CIs. This is true enough, but such structure in the data, when the designers are humans, is very limited – all of this was thoroughly discussed years ago by Doug Theobald in his discussion of natural versus artificial hierarchies, in his 29+ Evidences for Common Ancestry FAQ, a resource which Luskin, Meyer et al. still lack the courage to engage with in any detail: http://www.talkorigins.org/faqs/com[…]ed_hierarchy

If Luskin specified a quantifiable model for ID that specified what parameters are to be learned from the data, and generated distributions of data (or CI or other statistics) from the model, then he’d have some shot at progressing in an anti-frequentist direction. But good luck with that – IDists rarely say anything specific enough about their designer to be subject to empirical test.

As for going beyond frequentist null-hypothesis rejection, us phylogeneticists got there years ago. Maximum likelihood and Bayesian methods are now dominant in the field (although only just starting in fossil invertebrate studies like the Cambrian; almost the last frontier for this area). For the sake of simplicity, I focused on parsimony/cladistic methods in my critiques of Darwin’s Doubt, and as a result of that, plus the IDists’ systematic naivety and amateurism, cladistics is almost all that gets talked about in the IDists’ replies. But if they would like tests of common ancestry in a fully likelihoodist or Bayesian framework, where null hypotheses do not have to be assumed at all, we’ve got that covered. Doug Theobald did that already (also), in his 2010 Nature paper testing common ancestry. We could do it for Cambrian morphology data matrices too, although it would take a couple of weeks of full-time work and thus a grant or a graduate student. Of course, the IDists just summarily rejected that work as well, so I’m not sure what the point would be.

Other loose points:

(5) Character states evolving twice. Luskin seems to think that any character state that evolves twice constitutes a contradiction of evolutionary expectations. So, under his view, under evolution, all character states of any sort, whether complex (wings, eyes) or simple (a bump on a bone, a bend in an exoskeleton plate) have to evolve once and only once, or else common ancestry is wrong and we should just conclude special creation instead. He seems to think that, under evolution, if a character can change states once, there must be some magical force that prevents a similar event from happening elsewhere somewhere else in the tree.

(6) Estimating phylogenies from characters that change more than once. And scotch. Luskin also seems to think that, if characters change states more than once, then the whole enterprise of estimating phylogenetic trees is hopeless and subjective. He ignores a point I made before, which is totally obvious when you think about it, that on any tree that is not tiny, characters that change twice on a tree will still have plenty of phylogenetic signal. In fact, we could easily simulate characters on a tree, give them an evolutionary rate high enough so that the expected amount of change is 2 changes per character on the tree, and then see if we can infer the tree given only the character states at the tips as data. It’s not even that interesting to run the experiment, because I know what the result would be: this would be an easy phylogenetic inference problem, given a reasonable number of taxa and reasonable number of characters. I’d even wager a bottle of single-malt scotch on it.

The real puzzle is why Luskin thinks that anyone who actually knows phylogenetics, and knows facts like the above, will take him seriously.

Various things I wish the IDists would get clear in their heads:

(7) Characters versus character states. They don’t get that characters can be homologous, even while character states can evolve convergently.

(8) Changing dating of the Cambrian. The dating of the beginning of the Cambrian, and key (although now outdated) subsets like the Tommotian, has been some of the least certain dating in the Phaenerozoic timescale. However, the IDists love to cite dating estimates from the mid-1990s that put the “appearance of ‘phyla’” (this whole phrase relies on ignoring the stem/crown distinction) in a particularly narrow time window. They also LOVE to conflate this period with the beginning of the Cambrian, and pretend that the history is basically: unicells, Ediacarans, boom-modern-phyla. This depiction of history is the dominant picture presented in Darwin’s Doubt. But, first, the estimates have broadened in the last two decades; second, relevant stuff was going on before the “appearance of ‘phyla’”, namely the diversification of the small shellies, still completely inadequately dealt with in Debating Darwin’s Doubt (there is no new material on them in the book); third, the small shellies go back into the late Precambrian, and do not themselves constitute the beginning of the Cambrian; and fourth, if one is phylogenetically rigorous about the crown/stem distinction, many “phyla” originate well after the “Explosion” – what you have in the Cambrian Explosion is mostly stem groups to the classic phyla, or groups on the stems of classes, etc.

(9) Cladistics isn’t the beginning and ending of phylogenetics. It’s more the beginning. Many of the limitations of “classic” cladistics (no direct ancestors, no consideration of time, equal weighting of characters etc.) don’t apply to statistical phylogenetics.

(10) And, pattern cladistics isn’t cladistics, it’s an almost-extinct subset of cladistics that was probably always in the minority. Quoting a stale bit of pattern cladistic dogma, whether from an alleged authority or something recycled in a textbook, does not prove anything except one’s quote-mining ability. In contrast to pattern cladistics, most modern researchers in phylogenetics think that cladograms and phylograms (and in the best case, chronograms) are an estimate of evolutionary history, not just a description of pattern and not just a method of classification. Most researchers similarly accept that having an estimate of the phylogenetic tree, which automatically includes an estimate of character evolution histories, also tells us many important things about the *processes* involved – speciation and extinction rates, correlations between characters and these rates, rates of change in character evolution and how those rates change through time (for example, major radiations into empty ecological niches, versus evolution in stable “filled” ecosystems), etc.

(11) It’s true that cladistics, or better, phylogenetics, doesn’t answer all questions of interest about the Cambrian Explosion, or anything else. BUT, FOR THE LOVE OF THE DESIGNER, THAT IS THE CASE FOR EVERY INVESTIGATIVE METHOD IN SCIENCE. Carbon dating tells you the age of organic material that is less than 50,000 years old, not the age of the Earth. Stratigraphy tells you relative age, not absolute age. Light microscopy can tell you what chromosomes are doing, but not the DNA sequence. Sequencing a genome tells you what the DNA sequence is, but doesn’t tell you what is functional, nor how your functional assessment would change if you looked at the highly-different genome sizes in related organisms (take note, ENCODE). Cladistics and phylogenetics, as I have said, give the big picture: in what order did character states change? How did the collection of character states that we now take to mean “phylum” assemble, character-change-by-character change? Other disciplines (evo-devo, molecular biology, population genetics) can then examine how individual characters change. When Luskin et al. whine that “cladistics doesn’t explain the origin of information”, the major response is: “No, you moron, molecular biology and population genetics explain the origin of new genetic information, especially gene duplication and modification of duplicates by mutation, drift, and selection.”

(Behe and Berlinski have already basically admitted that evolutionary biologists have reasonably and successfully explained the origin of at least some new genes with these processes, fatally sinking much of the Luskin/Meyer’s core arguments on this topic. This conflict is unaddressed in Debating Darwin’s Doubt.)

Melting of polar ice. Mr. Moore writes, “Our ship got caught in the ice and had to be freed by a Canadian ice breaker. Global warming – what?? Actually, yes – we could not get through because so much ice broke free further north near the polar ice cap and was blown south into the shipping channels.” Mr. Moore will receive a signed copy of Why Evolution Works (and Creationism Fails), which has been donated by one of the authors.

Spiderman Shpiderman – a penpal of mine, who can identify himself if he likes (I will of course understand if he demurs), asks,

There’s a lot of excitement and amazement about the lack of cratering and the height and sharpness of the geological features on Pluto. It appears that, contrary to earlier speculation, Pluto is geologically active and thus geologically young…though “young” in the sense that these features are probably less than 100 million years old.

Now that the results are in, how long do you think it’ll be until AIG posts something about how a “Young Pluto Supports Recent Creation” and “Secular scientists with atheistic uniformitarian assumptions predicted that Pluto would be a dead planet pockmarked by craters, but the evidence of recent geologic activity should come as no surprise to Christians, who know that Pluto was created along with all the other celestial bodies on the Fourth Day just over 6,000 years ago!”

The closest approach of the New Horizons spacecraft was last Tuesday, around noon UTC, and my penpal wrote, “I will give them until Friday morning.” Friday has come and gone, and Saturday is nearly gone in Kentucky, but the latest post from AIG concerns the burning question of whether Spiderman really exists.

Perhaps the AIG-ites can use a little help. We invite our readers to suggest explanations (post hoc, of course, and within a creationist framework) for why Pluto and Charon are geologically active even though they are so small and so distant from the Sun.

We also suggest a Pluto Pool, wherein our readers try to guess the date and time of AIG’s first comment on the fascinating geology of Pluto and Charon. The winner of the pool is the person who most closely predicts the correct date and time, but whose prediction predates that date and time. Entry into the pool costs nothing, and the winner receives a commensurate amount, because AIG’s comment on the subject is bound to be worth that amount.

I do not know what to make of this, but UPI reports that a team from the University of Northumbria, “saying they understand solar cycles better than ever, predict that the sun’s normal activity will decrease by 60 percent around 2030 – triggering the ‘mini ice age’ that could last for a decade.” That sentence is unclear, but I presume they mean “normal sunspot activity.” As they do not quite say, the northern hemisphere (at least) experienced the Little Ice Age about 300 years ago. The Little Ice Age corresponded with a period of minimal sunspot activity known as the Maunder minimum, and Wikipedia states that a causal connection has recently been established.

Nothing in this report contradicts conclusions about climate change and anthropogenic global warming. Nevertheless, expect climate-change deniers to have a field day!

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Why are giant pandas so lazy?tag:pandasthumb.org,2015://2.71122015-07-10T16:14:24Z2015-07-10T17:15:51ZProfessor Steve Steve informs us of an article Why are pandas so lazy? in Science Now. Professor Steve Steve takes exception to the claim that he is lazy. Yes, it is true that the giant panda’s daily energy expenditure is about 5 MJ: roughly one-third that of a dog and about the same as a three-toed sloth. It is also true that Professor Steve Steve moves slowly and basks a lot in the sun. Why?...Matt Younghttp://www.mines.edu/~mmyoung

Professor Steve Steve informs us of an article Why are pandas so lazy? in Science Now. Professor Steve Steve takes exception to the claim that he is lazy. Yes, it is true that the giant panda’s daily energy expenditure is about 5 MJ: roughly one-third that of a dog and about the same as a three-toed sloth. It is also true that Professor Steve Steve moves slowly and basks a lot in the sun. Why? Because the giant panda is a carnivore that survives on a low-energy plant diet, which his body is ill-equipped to digest. To conserve energy, he maintains a low body temperature, and his organs, including his brain, are small.

Professor Steve Steve demurs. He claims that he is not lazy; he is simply ruminating.

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Photography Contest VII: Finaliststag:pandasthumb.org,2015://2.71092015-07-06T18:00:00Z2015-07-17T18:33:44ZHere are the finalists of the 2015 photography contest. We received 16 photographs from 7 photographers, somewhat fewer than in previous years. This year we decided to choose 1 picture from each entrant and enlisted our wife to help with the choices. The text was written by the photographers and lightly edited for consistency. The finalists are given below the proverbial fold, in alphabetical order of last name. Please look through their photographs before voting...Matt Younghttp://www.mines.edu/~mmyoung

Here are the finalists of the 2015 photography contest. We received 16 photographs from 7 photographers, somewhat fewer than in previous years. This year we decided to choose 1 picture from each entrant and enlisted our wife to help with the choices. The text was written by the photographers and lightly edited for consistency.

The finalists are given below the proverbial fold, in alphabetical order of last name. Please look through their photographs before voting for your favorite. You will have to be logged in to vote on the poll. We know it is possible to game these polls. Please be responsible and vote only once. If we think that the results are invalid, we will cancel the contest.

Larval feeding galleries of Agrilus planipennis Fairmaire – emerald ash borer. They are an invasive species in the American Upper Midwest (arriving here from Asia some fifteen years ago) that poses a serious threat to the native population of ash trees (genus Fraxinus). Some of their opportunistic enemies (e.g., woodpeckers and squirrels) inflict their own damage on the trees as they search for the larvae. Their spread is aided by human transport of infected wood, especially as firewood.

Felis catus – domesticated cat. Mr. Pavlov tells us, “The photo of the cat is my cat Rosie, short for Rosen of Einstein-Podolsky-Rosen (her sister is named Electron, not pictured). She is a daughter of a feral cat, rescued from a swamp in central Louisiana.”

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The leap second and the creationisttag:pandasthumb.org,2015://2.71072015-06-27T21:33:04Z2015-06-28T01:13:02ZI have got to stop following links in e-mails from AIG. Today I read the most bizarre article by Dr. Danny Faulkner, an astrophysicist who must have slept through his celestial mechanics courses. Dr. Faulkner discusses the leap second that will be added at 23:59:59 UTC (GMT) on June 30. He notes correctly that the rotation of the Earth is slowing down, and the moon is consequently drifting farther from the Earth. He then observes,...Matt Younghttp://www.mines.edu/~mmyoung

I have got to stop following links in e-mails from AIG. Today I read the most bizarre article by Dr. Danny Faulkner, an astrophysicist who must have slept through his celestial mechanics courses. Dr. Faulkner discusses the leap second that will be added at 23:59:59 UTC (GMT) on June 30. He notes correctly that the rotation of the Earth is slowing down, and the moon is consequently drifting farther from the Earth. He then observes,

Finally, there is a long-term secular (non-periodic) slowing in the earth’s rotation caused by the tidal interaction of the earth and moon. As the earth slows its rotation, the moon spirals away from the earth. Therefore, in the past the earth spun more rapidly and the moon was much closer to the earth. Direct computation shows that the earth and moon would have been in contact about 1.3 billion years ago. Even a billion years ago the moon would have been so close to the earth that tides would have been a mile high. No one–including those who believe that the earth is far older than a billion years–thinks that tides were ever that high or that the moon and the earth touched a little more than a billion years ago.

However, since the earth and moon are only thousands of years old as the Bible clearly indicates, the long-term change in the earth-moon system is no problem. Indeed, what we see in the interaction between the earth and moon offers powerful evidence that the earth and moon are young.

I do not know the nature of the “direct computation,” but I would bet that it is based on the radius of the moon’s orbit increasing at a constant rate. Not obviously a good assumption; an article from Cornell University (which has a scientific reputation at least as distinguished as that of AIG) notes,

The exact rate of the Moon’s movement away from Earth has varied a lot over time. It depends both on the distance between the Earth and the Moon, and the exact shape of the Earth. The details of continents and oceans moving around on Earth actually change the rate, which make it a very hard thing to estimate. The rate is currently slowing down slightly, .…

Worse, look at Dr. Faulkner’s statement that “the earth and moon would have been in contact about 1.3 billion years ago.” An absolutely remarkable statement from a person who purports to have a PhD in physics and astronomy! Has he never heard of Roche’s limit? Roche’s limit is the smallest radius that a large satellite can maintain without being torn apart by tidal forces caused by the gravitational field of the main planet. According to NASA, Roche’s limit for the Moon is about 20 000 km, so I can assure Dr. Faulkner that the Earth and the Moon have never been in contact – not 1.3 billion years ago, not ever. When the Moon was formed, it had to have been formed outside Roche’s limit, and then it drifted away from the Earth at a rate that is not a constant and therefore not amenable to simple calculations.

Modern astronomy is not threatened, and the Earth is not young.

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Zack Kopplin gets nice write-up in Mother Jonestag:pandasthumb.org,2015://2.71062015-06-26T14:39:19Z2015-06-26T15:39:19ZYou can read it for yourself here. But, for my money, Mr. Kopplin exposes Gov. Bobby Jindal’s inner hypocrite with these too kind words: “I mean, who knows? I could be totally wrong, and maybe Jindal believes this [creationism] with his whole heart. Which is more why I go back to what his kids are learning. I had their seventh-grade biology teacher at [University Laboratory School] where I went for middle school, and I know...Matt Younghttp://www.mines.edu/~mmyoung

“I mean, who knows? I could be totally wrong, and maybe Jindal believes this [creationism] with his whole heart. Which is more why I go back to what his kids are learning. I had their seventh-grade biology teacher at [University Laboratory School] where I went for middle school, and I know she doesn’t just teach evolution–she’s absolutely obsessive about it. If Jindal actually was a creationist, I think he’d have a much bigger problem with his kids being taught what evolution is.”

Mr. Kopplin, who is on the verge of graduating from Rice University,

has continued to beat the drum on what he views as the erosion of public schools. He has broadened his focus to include the governor’s voucher program, which diverts state money to religious schools that question evolution and openly discriminate against students who violate their moral code. … And Kopplin has expanded his push to Texas, where he discovered that students at the state’s biggest charter school network were being taught that the “sketchy” fossil record undermines the theory of evolution.

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Will AIG return the Allosaurus fossil?tag:pandasthumb.org,2015://2.71052015-06-23T14:57:26Z2015-06-23T15:57:26ZDan Phelps alerted us to the fact that AIG’s Allosaurus fossil had been donated by an organization headed by Michael Peroutka, a man affiliated with “a white supremacist, neo-Confederate and pro-secessionist organization that has been named a hate group by the Southern Poverty Law Center.” Mr. Phelps now writes, Interesting that this press release didn’t get any coverage when I sent out the information last year. The Creation Museum received an Allosaurus dinosaur fossil appraised...Matt Younghttp://www.mines.edu/~mmyoung

Dan Phelps alerted us to the fact that AIG’s Allosaurus fossil had been donated by an organization headed by Michael Peroutka, a man affiliated with “a white supremacist, neo-Confederate and pro-secessionist organization that has been named a hate group by the Southern Poverty Law Center.” Mr. Phelps now writes,

Answers in Genesis (the owners of the Creation Museum) admirably makes anti-racist statements at times, but has taken a valuable donation from Michael Peroutka, a former Board Member of the racist hate group known as the League of the South. Why doesn’t the Creation Museum return the fossil or give it to a real science museum?

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Unidentified fossiltag:pandasthumb.org,2015://2.71042015-06-22T18:00:00Z2015-06-20T17:47:13Z David MacMillan, who wrote an 8-part series on creationism for us, sent us these 4 photographs, along with the following request: “I recently moved back to central Kentucky. One of the things I came across while visiting my family was this fossilized object I discovered near my home here when I was about 9 or 10 years old. “Back in the late 90s, we were living in a new development and there was a...Matt Younghttp://www.mines.edu/~mmyoung

“I recently moved back to central Kentucky. One of the things I came across while visiting my family was this fossilized object I discovered near my home here when I was about 9 or 10 years old.

“Back in the late 90s, we were living in a new development and there was a lot of excavation going on near our house. I believe I found this half-buried in the bottom of a rain-fed creek just after a particularly heavy period of excavation followed by some heavy rainstorms.

“It appears to be a vertebra, due to the shape and orientation of the various spurs, and what seems to be a very large nerve opening going in the side. The exterior is dotted with what appear to be marine fossil concretions, including scallops and similar creatures.

“This region of Kentucky comprises primarily Ordovician limestone and shales, which is puzzling because this would have to be a pretty large marine vertebrate, and there were virtually no large bony vertebrates in the Ordovician. Perhaps this is actually not a vertebra at all and is rather some sort of oddly-shaped shell?

“The largest human lumbar vertebrae are around 13 mm thick, while this measures over 5 cm thick. If it is a vertebra, it would have to come from an animal with a spinal column at least five times the length of a human spine.

“Basically, I’m stumped. Any idea whether any of the readers of Panda’s Thumb might be able to identify it?”

Ondatra zibethicus – muskrat, Elmer’s Two-Mile Creek, Boulder, Colorado, May, 2015. The muskrat shown here disappeared after the 2013 flood, and I did not see any muskrats again till this spring.

Don’t forget to enter the photography contest – 1 week remaining!

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Is Justice Scalia a creationist?tag:pandasthumb.org,2015://2.71032015-06-10T17:02:33Z2015-06-10T18:04:11ZThe Washington Post reported the other day that Justice Antonin Scalia, in a commencement address, said, Humanity has been around for at least some 5,000 years or so, and I doubt that the basic challenges as confronted are any worse now, or alas even much different, from what they ever were. I suppose that “at least 5000 years” gives you some wiggle room, but I would hardly call, say, 200,000 years “at least 5000 years.”...Matt Younghttp://www.mines.edu/~mmyoung

The Washington Post reported the other day that Justice Antonin Scalia, in a commencement address, said,

Humanity has been around for at least some 5,000 years or so, and I doubt that the basic challenges as confronted are any worse now, or alas even much different, from what they ever were.

I suppose that “at least 5000 years” gives you some wiggle room, but I would hardly call, say, 200,000 years “at least 5000 years.” That is a bit like saying, “The trip from Boulder to New York is at least 20 kilometers.”

Jerry Coyne, who is much nicer than I am, thinks that it might have been “just an offhand remark that’s been blown out of proportion.” Well, maybe, but I watched most of the speech on Professor Coyne’s website, and I could not help but notice that Justice Scalia was reading that text: he did not misspeak.

Justice Scalia dissented in Edwards vs. Aguillar, but he seemed more concerned with whether the legislature intended creation “science” as a religious doctrine than with its scientific merit. He also supported the “balanced treatment” argument to the effect that students who learn evolution are entitled to the opposing view as well. His argument was well reasoned but depended on the assumption that creation science is not a religious doctrine if its supporters think it is not.

Contrary to some reports, Justice Scalia did not say, “The body of scientific evidence supporting creation science is as strong as that supporting evolution”; rather, he was paraphrasing the testimony of witnesses and states explicitly “that I by no means intend to endorse its accuracy” but that “what is crucial is not [the legislature’s] wisdom in believing that [a certain secular] purpose would be achieved by the bill, but their sincerity in believing it would be” [italics in original].

Still, Justice Scalia generally comes across as an authoritarian, uncomfortable with ambiguity and guided by literalist interpretations. If he takes the Bible as literally as he takes the Constitution, then it is easy to see that he might well believe in a young Earth. I hope I am wrong and Professor Coyne is right.